#include <aligner.h>
Inheritance diagram for EMAN::RotationalAlignerIterative:
Public Member Functions | |
virtual EMData * | align (EMData *this_img, EMData *to_img, const string &cmp_name="dot", const Dict &cmp_params=Dict()) const |
To align 'this_img' with another image passed in through its parameters. | |
virtual EMData * | align (EMData *this_img, EMData *to_img) const |
virtual string | get_name () const |
Get the Aligner's name. | |
virtual string | get_desc () const |
virtual TypeDict | get_param_types () const |
Static Public Member Functions | |
Aligner * | NEW () |
Static Public Attributes | |
const string | NAME = "rotational_iterative" |
The advantage of this over the 'regular' rotational alinger is that this is done in real space and does not use invariants.
r1 | inner ring | |
r2 | outer ring |
Definition at line 330 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 336 of file aligner.h. References align(). 00337 { 00338 return align(this_img, to_img, "dot", Dict()); 00339 }
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To align 'this_img' with another image passed in through its parameters. The alignment uses a user-given comparison method to compare the two images. If none is given, a default one is used.
Implements EMAN::Aligner. Definition at line 532 of file aligner.cpp. References EMAN::EMData::calc_ccfx(), data, EMAN::Util::find_max(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), and EMAN::EMData::unwrap(). 00534 { 00535 int r1 = params.set_default("r1",-1); 00536 int r2 = params.set_default("r2",-1); 00537 //to start lest try the original size image. If needed, we can pad it.... 00538 EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true); 00539 EMData * this_img_polar = this_img->unwrap(r1,r2,-1,0,0,true); 00540 int this_img_polar_nx = this_img_polar->get_xsize(); 00541 00542 EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img->get_ysize()); 00543 00544 //take out the garbage 00545 delete to_polar; to_polar = 0; 00546 delete this_img_polar; this_img_polar = 0; 00547 00548 float * data = cf->get_data(); 00549 float peak = 0; 00550 int peak_index = 0; 00551 Util::find_max(data, this_img_polar_nx, &peak, &peak_index); 00552 00553 delete cf; cf = 0; 00554 float rot_angle = (float) (peak_index * 360.0f / this_img_polar_nx); 00555 00556 //return the result 00557 //cout << rot_angle << endl; 00558 Transform tmp(Dict("type","2d","alpha",rot_angle)); 00559 EMData * rotimg=this_img->process("xform",Dict("transform",(Transform*)&tmp)); 00560 rotimg->set_attr("xform.align2d",&tmp); 00561 00562 return rotimg; 00563 00564 }
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Implements EMAN::Aligner. Definition at line 346 of file aligner.h. 00347 { 00348 return "Performs rotational alignment using the SPIDER method"; 00349 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 341 of file aligner.h. 00342 {
00343 return NAME;
00344 }
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Implements EMAN::Aligner. Definition at line 356 of file aligner.h. References EMAN::TypeDict::put(). 00357 { 00358 TypeDict d; 00359 d.put("r1", EMObject::INT, "Inner ring, pixels"); 00360 d.put("r2", EMObject::INT, "Outer ring, pixels"); 00361 return d; 00362 }
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Definition at line 351 of file aligner.h. 00352 { 00353 return new RotationalAlignerIterative(); 00354 }
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Definition at line 61 of file aligner.cpp. |